"The Fall of the Mutants" was a comic bookcrossover event by Marvel Comics spanning January to March 1988. It spanned three issues each of The Uncanny X-Men (issues #225–227), X-Factor (issues #24–26), and The New Mutants (issues #59–61); unlike most crossovers however, the various titles' storylines did not intertwine, but were instead linked thematically as each team underwent major ordeals and drastic changes in their status quo.

Marvel Comics used a novel approach in advertising the crossover event. A major element within the stories at the time was the public's growing concern over the "mutant menace" and Senator Robert Kelly's proposed Mutant Registration Act, which foreshadowed the dystopian future shown in "Days of Future Past". Marvel distributed postcard-size mock advertisements supporting the act in comic book stores as well as their various titles cover dated "November 1987". Asking "Do You Know What Your Children Are?", the card further suggested that anyone who knew themselves to be a mutant should fill out the form on the back and mail it in to register themselves with the government.

The X-Men head to Dallas, Texas in search of their missing and de-powered leader Storm, herself seeking the mutant inventor Forge to restore her powers. Upon arrival, they encounter Freedom Force, a government-sanctioned strike team of reformed villains led by Mystique, who are under orders to arrest the X-Men for refusing to comply with the Mutant Registration Act, and a fight ensues. Freedom Force's mutant precogDestiny then has a vision: everyone inside a particular Dallas skyscraper at dawn will be dead. Once it begins snowing - in Texas, in the middle of summer - and as cavemen, dinosaurs, and other strange peoples and creatures begin appearing, the two teams realize that something of immense gravity is going on. Calling a temporary truce, they turn to restoring order to the chaos engulfing the city. Many of the events are broadcast on television by reporter Neal Conan and cameraman Manoli Wetherell, who accompany the X-Men and Freedom Force.

Storm and Forge meanwhile find themselves in a pristine, natural world all to themselves. In this new Earth, time proceeds at an accelerated rate, and while only a few moments pass in the main reality, a year does for them. Storm, still hating the man she once loved (as Forge invented the Neutralizer gun that removed her mutant powers),[1] spends most of the year in solitude until she is finally ready to make her peace with him. Forge meanwhile had been developing technology from the ground up, eventually creating the tools - and with circuitry sourced from dismantling his bionic arm and leg - enabling him to build a device which restores Storm's weather manipulation powers. Storm, after months of being grounded takes to the skies again with joy, and Forge uses his shamanic magic in conjunction with her lightning bolts to open a portal back to Dallas.

Time and space meanwhile runs amok in the city, as the X-Men and Freedom Force find themselves amidst a scene from the Vietnam War. It is revealed that during his tour of duty, Forge had used his shamanic powers to summon a demon to avenge his fallen comrades. However, in his naiveté, he did not realize that the spell required the souls of his nine comrades, and unleashed a horde of demons he had no way to control, including the Adversary, the creature responsible for the chaos they now found themselves in.

As Storm and Forge join the battle, it quickly becomes apparent that the Adversary cannot be defeated, and the only way to be rid of him is for Forge to cast the same spell and seal him away forever. Millions watch the television broadcast (including a horrified Kitty Pryde) as Forge casts the spell, using the souls of the nine X-Men (Storm, Wolverine, Colossus, Longshot, Rogue, Dazzler, Psylocke, Havok, and Cyclops' estranged wife Madelyne Pryor) to fuel it. As foreseen by Destiny, the X-Men die. However, the goddess Roma, who'd also become embroiled in the day's events, takes pity on the X-Men for their noble sacrifice and returns them all to life, additionally commenting to them that as foul and evil as the Adversary is, he should not and cannot be locked away forever, since from the chaos he creates positive change and growth occurs. However, he was bound for an age, which Roma decreed was sufficient punishment for his crime. She additionally made the X-Men invisible to all forms of surveillance save plain sight, thus allowing them to continue with their operations while the world assumes they are dead. Before they head to Australia to establish a new base, she gives them the Siege Perilous, telling them they could use it to 'reset' time should they be discovered.

X-Factor (Cyclops, Marvel Girl, Beast, Iceman and Caliban) is transported to the Ship of the villain Apocalypse. Offered a place by his side in his evolutionary war against humans, they refuse, and a battle ensues between X-Factor and his Four Horsemen. The horseman Death then reveals himself to be their former teammate Angel, thought dead and now remade in Apocalypse's image with deadly, razor-sharp wings. He quickly defeats the team and they are restrained save for Caliban, who surrenders himself to Apocalypse in return for powers like Death. Apocalypse then unleashes his Horsemen on New York City and tries to force the heroes to watch. They are able to break free of their restraints, and attempt to stop the Horseman. In the process, they accidentally cause Apocalypse's airship to lose control, damaging several skyscrapers as it loses altitude. The preteen superhero team Power Pack helps limit the damage, destroying part of the airship's engine cowling just before the cowling would have impacted the Statue of Liberty. As the team battles the Horsemen, Iceman comes up with an idea to stop Death, and creates a statue of himself out of ice. Death attacks and breaks the statue and, thinking it is actually Iceman, is overcome with guilt and switches sides. Apocalypse easily repels his attacks, but decides to make a tactical withdrawal anyway. After he leaves, the team attempts to regain control of Apocalypse's airship, eventually bringing it to land on top of their headquarters, crushing it.

The New Mutants (Cannonball, Cypher, Magik, Mirage, Sunspot, Warlock, and Wolfsbane) head off to visit their friend Bird-Brain on his remote island. There, they quickly discover that Bird-Brain's creator, the Ani-Mator, is creating more semi-sentient creatures (the Ani-Mates), which he mistreats and experiments on. As the team attempts to free them, the anti-mutant organization known as the Right tracks them down and attacks. During the three-pronged battle, Cypher is shot and killed, taking a bullet meant for Wolfsbane. Eventually, Bird-Brain defeats the Ani-Mator and becomes king of the Ani-Mates, and Magik teleports the Right's soldiers, along with the Ani-Mator himself, to Limbo. They then return home, where Magneto (headmaster of the Xavier School in Professor X's absence) blames humanity for Cypher's death. Disgusted, the team quits Magneto's tutelage, while deciding to stay dedicated to Professor X's dream of peace.

While not officially part of the crossover, a number of other Marvel comic books were billed as "Fall of the Mutants" Tie-Ins:

Captain America #339

As a reward for defeating Marvel Girl, Apocalypse teleports his Horseman Famine to the American midwest to destroy its crops and cattle with her life-draining powers. Steve Rogers (who had at the time given up the uniform of Captain America and was simply operating as "The Captain"), along with allies Nomad, Falcon and D-Man, fight and bring an end to her attack on "America's bread basket".

Daredevil #252

Apocalypse's attack on New York City brings chaos and looting to its streets, with many citizens thinking a nuclear attack has occurred. Daredevil and the Black Widow do their part to restore order.

Power Pack #35

The children of Power Pack become involved in the chaos of Apocalypse's attack on the city and come into conflict with the Horseman Pestilence. Pestilence dies when part of the Empire State Building falls on her, but not before she infects Katie Power. This sickness spreads to her siblings, but the Pack overcome the affliction by initiating their healing talents together.

Fantastic Four #312

After the ticker-tape parade honoring X-Factor for saving the city from Apocalypse and his Horsemen, the team help the Fantastic Four defeat Doctor Doom.

Hulk #340

Wolverine fights the Hulk while the X-Men are flying in their Blackbird to Dallas. The comic does not have the 'Fall of the Mutants Tie-In' logo on the cover despite being advertised as such.